Pretty errors, warnings and messages in R Markdown

June 18, 2017
By

[This article was first published on R on Tea & Stats, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
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When knitting an R Markdown document to HTML output, R chunks can produce warnings, errors or messages.

Normally these messages look like any other console output:

R Markdown alert messages

Pretty ugly, and usually something I find myself trying to hide at the earliest opportunity.

But if you’re using R Markdown’s default template, which uses Twitter Bootstrap, you can promote warnings, errors and messages to first-class citizens.

What if you could have them looking like this?

Bootstrap-styled alert messages

Bootstrap includes dedicated message boxes for danger, warnings and information.
If you were writing an ordinary web site, you would generate these using the following HTML markup:

Danger: This is a warning!

You can achieve this in R Markdown using knitr chunk hooks.
Just add the following code to a chunk near the start of your .Rmd file.

knitr::knit_hooks$set(
   error = function(x, options) {
     paste('\n\n
', gsub('##', '\n', gsub('^##\ Error', '**Error**', x)), '
', sep = '\n') }, warning = function(x, options) { paste('\n\n
', gsub('##', '\n', gsub('^##\ Warning:', '**Warning**', x)), '
', sep = '\n') }, message = function(x, options) { paste('\n\n
', gsub('##', '\n', x), '
', sep = '\n') } )

And you’re done! For a full demonstration and further details, read this vignette.

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